Covalent bond : electron pairs are shared between atoms .
Non – Covalent bonds :
1) Ionic bonds : result from the electrostatic attraction between two ionized groups of opposite charge.
2) Hydrogen bounding : is an attraction between hydrogen atom covalently bounded to highly electronegative atom on a second electronegative atom
3) Vander Waals Forces : are short range attractive forces. Vander Waals forces are weaker than ionic and hydrogen bonding.
Intermolecular force : is an attraction. The net attraction is the sum of pair of interactions between the molecules.
4) Hydrophobic Interactions : Molecules such as proteins have polar and nonpolar groups.
polar groups : have tendency to be solvated in water.
nonpolar groups : do not have tendency to contact with water.
Amino Acids : are the building blocks of proteins.
1) Nonpolar or Hydrophobic R groups
2) Unchanged , neutral R groups
3) Polar negatively charged R groups
4) Polar positive charged R groups
Properties of Amino Acids :
1) They are white crystillane substances.
2) They are much soluble in water than nonpolar ( organic ) solvent.
3) Net charge , solubility , reactivity in chemical rxn and acception behaviour of amino acids is related to the chemical nature of R groups. The solubility of proteins in water is related to essentially to the distribution of the polar and nonpolar groups of the side chain
4) Crystalline amino acids have relatively high melting points ( above 200 ). Ionic compounds exhibith high melting points because all the strong ionic attraction between the ionized groups.
5) Aminoacids in neutral aqeous solutions have both positive and negative charges.
A dipolar ion of any amino acid act as an acid ( proton donor ) as a base ( proton accepter )
Any molecule containing both groups and being able to act as an acid or a base is called an amphoteric molecule.
PEPTIDE: small # of AA linked in defined sequence.
In proteins , the – carboxyl groups of one AA is joined to the -amino group of other amino acid by peptide bond.
Disulfide Bond :
-SH ( sulfydryl group ) is highly reactive.
Properties of Peptides :
1) Usually high melting points
2) – carboxyl groups and -amino groups in the peptide linkages can not ionize in the ph zone from 0 to 14
3) Acid – Base properties of peptides are determined by free -amino group of the N-terminal residue , the free -carboxyl group of C-terminal residue and those R groups of the residues which can ionize.
4) Give the avarage elemental composition of proteins basis of the percent C,N,H,O …
Conformation of Polypeptide Chains:
1) Primary Structure: involves the sequenced amino acids. Zig-zag shape with R groups protruding in opposite directions. NH group does not protonate between pH 0 to 14. The C-N link is not able to rotate freely ( very stable ).
CO-NH atoms involved in the peptide bond and two -C atoms are in the sample plane. A series of rigid planes are seperated by HCR groups.
The primary structured proteins are determined by breaking the peptide bond by hydrolysis reactions under the catalytic activity of enzymes or by acid hydrolysis.
2) Secondary Structure : H bonding between O and H of amino group.
· – helix
· -plated sheet parallel , anti-parallel
–helix structure : is governed by intramolecular H – bonding. -helix structure
is an ordered particularly stable structure. Side chains are located outside of the helix. Each peptide bond is engaged in the formation of H – bond , the helixal structure has hight stability and this structure resricts the H bonding with other molecules esp with water.
-plated sheet : a rises from the intermolecular H bonding. The side chains are located above and beneath the plane of the sheets , and their charges and long R groups have a little effect on the structure.
3) Tertiary Structure : non-covalent interactions if chains
· electrostatic interactions
· hydrogen bonding
· vander waals interaction
· interactional non-polar side chains
· disulfide bonds
4) Quaternary Structure : non-covalent associate ion of polypeptide. chain subunits >> identical subunits , different subunits.
Denaturation Of Proteins : ( change in the protein conformation ) Acid , alkali , concentrated soline solutions , heat , radiation.
Protein denaturation is modification of secondary , tertiary or quaternary structure not accompained by the rupture of peptide bonds involved in the primary structure.
Pysical Agents :
· Mechanical Treatment
· Heigh pressure
· Interfaces : adsorption at the interface >> irreversible denaturation
o electromagnetic radiation
o ultraviolet radiation is observed by aromatic a.a residues.
Chemical Agents :
· Acid and alkalies
· Organic solvents
· Aq. solutions of organic compounds urea , Quanidine salt
· Quanidine Hydrochloride and Ures are widely used denaturating agents used for the preparation of partially unfolded proteins.
Determination of Sequence of Amino Acids:
Break All Cys-S-S-Cys disulfide bonds : mercaptoethonol urea used to cleaves all S-S bond
Determine the amino acid composition : 6N HCI for abouth 20-24 hrs at 100 C all peptide bonds are broken down. Aminoacids >> molar ratios are determined by aminoacids analysis. Ninhydrin and fluorescomine are used for detection of a.a
Identıfy N-terminal and C-terminal a.a :
Identification of N terminal a.a : Edman degradation and Sanger’s methot used.Edman reagent is Pheynlisothiocyanate and sanger’s method reagent is fluorodinitrobenzene.
Identification of C terminal a.a : Carboxypeptidase and hydrazine are used to determine C – terminal a.a because both enzymes do not react.
Break polypeptides into fragments , determine the a.a composition of each fragment
Determine a.a sequence of each fragment and determine sequence of polypeptide.
Lorate S-S bond